With the example plugin (https://github.com/MilkBowl/VaultExamplePlugin/blob/master/src/com/vault/example/plugin/ExamplePlugin.java)
I get
The method .....() is undefined for the type Vault
for every method that is called from vault

Try this snippet of code instead:

    RegisteredServiceProvider<Permission> permissionProvider = getServer().getServicesManager().getRegistration(net.milkbowl.vault.permission.Permission.class);
    if (permissionProvider != null) {
        permission = permissionProvider.getProvider();
    }

example plugin is outdated.

Can I find an updated example somewhere?
I replaced the permissionProvider part with mung3r's suggestion but I still cant get it to work.

@Armarr - the Vault overview page on DBO tells exactly how to link the Permission API - if you need more help please post up on the forums there asking for help to get it working, thanks a bunch and hopefully you'll be able to get it working!